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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
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Gordon Smyth
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Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.
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You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies.
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The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
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Thanks for responding! I did change the code slightly:
dge1 <- DGEList(counts = combined_data_counts)
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The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1).
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